Research workbench
Sn-glycerol-3-phosphate binding periplasmic protein ugpb from escherichia COLI - W169S, W172S
Analyse Sn-glycerol-3-phosphate binding periplasmic protein ugpb from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X84
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sn-glycerol-3-phosphate-binding periplasmic protein ugpb
- UniProt
- P0AG80
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sn-glycerol-3-phosphate-binding periplasmic protein ugpb | protein | 416 | 50% helix, 17% strand | P0AG80 |
| B | Sn-glycerol-3-phosphate-binding periplasmic protein ugpb | protein | 414 | 50% helix, 16% strand | P0AG80 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.73 | 0.81 | 54 | empty |
| 2 | 56 | 0.72 | 0.98 | 24 | empty |
| 3 | 453 | 0.62 | 0.76 | 49 | empty |
| 4 | 386 | 0.60 | 0.77 | 45 | empty |
| 5 | 88 | 0.59 | 0.88 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6X84 · Sn-glycerol-3-phosphate binding periplasmic protein UgpB from Escherichia coli - W169S… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AG80 · AlphaFold monomer V2.0 prediction for sn-glycerol-3-phosphate-binding periplasmic protein… · a predicted model of the same protein · chain B against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0AG80
- Elsewhere: RCSB PDB 6X84 · PDBe 6X84 · UniProt P0AG80
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